Diesel Engine Surveys
Calder's Marine Diesel Engines book has a nice DIY engine survey process. Many good tips/tricks but I can't imagine a boat owner being willing to let anyone (engine surveyer included) disassemble anything, even exhaust hose connections. It's just too easy for something simple to become a larger problem especially on older engines. Even oil analysis requires multiple samples over time to be useful barring some super serious issue. I think it's reasonable to question the utility of an engine survey at all.
The sea trial is a great tool for checking the engine. Smoke color at cold start-up, rattle/vibrations through the RPM range, RPM under load, acceleration/de-acceleration, temperature, etc. Talking to the owner and getting a feel for their knowledge and maintenance habits also provides some indicators. It's also good to do thorough homework on the specific engine models as most issues are well known in older models and you can focus on those, ask the owner, or check for the necessary fixes.
As others have noted the OP's specific failure mode was probably undetectable unless the pending failure manifest itself in some observable/measurable way. I was unaware of the shaft rotation trick. Might be nice if someone would compile a list of non-destructive/disassembly approaches for identifying engine issues that would be doable during a boat viewing.